Methods for nuclear extraction and amplification using a bio-field programmable gate array

Abstract

Disclosed herein are methods for nuclear extraction and amplification using a bio-field programmable gate array. The method includes disposing a mixed droplet including one or more target nucleic acids adsorbed to magnetic beads on a microelectrode array including microelectrodes operable to form one or more actuated patterns. The method includes extracting the one or more target nucleic acids from the mixed droplet by attracting the one or more target nucleic acids using magnetic force generated by one or more coils under the microelectrodes, and switching one or more of the microelectrodes corresponding to a disposal actuated pattern to move the mixed droplet to a disposal location. The method includes merging the one or more target nucleic acids and an amplifying droplet to form a pre-amplifying droplet, heating the pre-amplifying droplet under a programmed temperature scheme to generate an amplified droplet, and visualizing the amplified droplet.

1 . A method for nuclear extraction and amplification using a bio-field programmable gate array comprising:
 disposing a mixed droplet at a first location on a microelectrode array, wherein
 the mixed droplet comprises one or more target nucleic acids, lysis buffer, and magnetic beads, wherein the one or more target nucleic acids adsorb to the magnetic beads, and 
 the microelectrode array comprises a plurality of microelectrodes arranged in an array and operable to form one or more actuated patterns, each microelectrode comprising: a heater under the microelectrode, and a coil under the microelectrode; 
   extracting the one or more target nucleic acids from the mixed droplet by
 attracting the one or more target nucleic acids absorbed to the magnetic beads using magnetic force generated by the coil under the first location, and 
 switching one or more of the plurality of microelectrodes corresponding to a disposal actuated pattern to move the mixed droplet to a disposal location on the microelectrode array; 
   merging the one or more target nucleic acids and an amplifying droplet to form a pre-amplifying droplet at the first location;   heating the pre-amplifying droplet, using the heater under the first location, under a programmed temperature scheme to generate an amplified droplet; and   visualizing the amplified droplet.   
     
     
         2 . The method of  claim 1 , wherein the mixed droplet is formed by
 disposing a sample droplet containing the one or more target nucleic acids on the microelectrode array;   disposing a reagent droplet comprising the magnetic beads and the lysis buffer on the microelectrode array;   merging the sample droplet and the reagent droplet, using a merging actuated pattern, to form a merged droplet; and   mixing the merged droplet to form a mixed droplet by applying biases on the microelectrodes under the merged droplet in a cycle order.   
     
     
         3 . The method of  claim 1 , wherein after disposing the mixed droplet, the method further comprises heating the mixed droplet, using the heater under the first location, at a lysis temperature. 
     
     
         4 . The method of  claim 1 , wherein before merging the one or more target nucleic acids and the amplifying droplet, the method further comprises decanting the mixed droplet by merging and splitting the one or more target nucleic acids with one or more decanting droplets using one or more decanting actuated patterns. 
     
     
         5 . The method of  claim 1 , wherein after extracting the one or more target nucleic acids from the mixed droplet, the method further comprises releasing the one or more target nucleic acids from the magnetic beads by adding a droplet of elution buffer to the one or more target nucleic acids absorbed to the magnetic beads. 
     
     
         6 . The method of  claim 1 , wherein the amplified droplet is visualized using an optical sensor, when the amplifying droplet comprises a fluorescence and a quencher. 
     
     
         7 . The method of  claim 1 , wherein the programmed temperature scheme is based on a loop-mediated isothermal amplification process or a polymerase chain reaction cycling process. 
     
     
         8 . The method of  claim 1 , wherein the mixed droplet further comprises antibodies to label the mixed droplet. 
     
     
         9 . The method of  claim 1 , wherein the magnetic beads comprise iron oxide, iron, or cobalt, and wherein the magnetic beads are coated with silica, amino groups, or carboxyl groups. 
     
     
         10 . The method of  claim 1 , wherein the amplifying droplet comprises one or more of a primer, a nucleotide, a polymerase, and a buffer. 
     
     
         11 . The method of  claim 1 , wherein the microelectrode array further comprises a capacitive sensor under each microelectrode, wherein the capacitive sensor detects a volume and location of a droplet. 
     
     
         12 . A non-transitory computer-readable medium for nuclear extraction and amplification using a bio-field programmable gate array that includes logic that, when executed by a computing device, causes the computing device to perform at least the following:
 detecting a mixed droplet at a first location on a microelectrode array using a capacitive sensor or an optical sensor, wherein
 the mixed droplet comprises one or more target nucleic acids, lysis buffer, and magnetic beads, wherein the one or more target nucleic acids adsorb to the magnetic beads, and 
 the microelectrode array comprises a plurality of microelectrodes arranged in an array and operable to form one or more actuated patterns, each microelectrode comprising: a heater under the microelectrode, a coil under the microelectrode, and a capacitive sensor under the microelectrode; 
   extracting one or more the target nucleic acids from the mixed droplet by
 attracting the one or more target nucleic acids absorbed to the magnetic beads using magnetic force generated by the coil under the first location, and 
 switching one or more of the plurality of microelectrodes corresponding to a disposal actuated pattern to move the mixed droplet to a disposal location on the microelectrode array; 
   merging the one or more target nucleic acids and an amplifying droplet to form a pre-amplifying droplet;   heating the pre-amplifying droplet, using the heater under the first location, under a programmed temperature scheme to generate an amplified droplet; and   visualizing the amplified droplet.   
     
     
         13 . The medium of  claim 12 , wherein the mixed droplet is formed by
 detecting a sample droplet containing the one or more target nucleic acids on the microelectrode array;   detecting a reagent droplet comprising the magnetic beads and the lysis buffer on the microelectrode array;   merging the sample droplet and the reagent droplet, using a merging actuated pattern, to form a merged droplet; and   mixing the merged droplet to form a mixed droplet by applying biases on the microelectrodes under the merged droplet in a cycle order.   
     
     
         14 . The medium of  claim 12 , wherein after detecting the mixed droplet, the method further comprises heating the mixed droplet, using the heater under the first location, at a lysis temperature. 
     
     
         15 . The medium of  claim 12 , wherein before merging the one or more target nucleic acids and the amplifying droplet, the method further comprises decanting the mixed droplet by merging and splitting the one or more target nucleic acids with one or more decanting droplets using one or more decanting actuated patterns. 
     
     
         16 . The medium of  claim 12 , wherein after extracting the one or more target nucleic acids from the mixed droplet, the method further comprises releasing the one or more target nucleic acids from the magnetic beads by adding a droplet of elution buffer to the one or more target nucleic acids absorbed to the magnetic beads. 
     
     
         17 . The medium of  claim 12 , wherein the amplified droplet is visualized using the optical sensor, when the amplifying droplet comprises a fluorescence and a quencher. 
     
     
         18 . The medium of  claim 12 , wherein the programmed temperature scheme is based on a loop-mediated isothermal amplification process or a polymerase chain reaction cycling process. 
     
     
         19 . The medium of  claim 12 , wherein the amplifying droplet comprises one or more of a primer, a nucleotide, a polymerase, and a buffer. 
     
     
         20 . The medium of  claim 12 , wherein the capacitive sensor or the optical sensor detects a volume and location of a droplet.